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<p>A new, free, open-source program is available: PACUPP, Pockets
And Cavities Using Pseudoatoms in Proteins.</p>
<p>You can see sample results at</p>
<p><a class="moz-txt-link-freetext" href="http://proteopedia.org/w/PACUPP:_Pockets_And_Cavities_Using_Pseudoatoms_in_Proteins">http://proteopedia.org/w/PACUPP:_Pockets_And_Cavities_Using_Pseudoatoms_in_Proteins</a></p>
<p>There are demonstrations in YouTube and a slideshow. You can find
these and download the program at <a class="moz-txt-link-freetext" href="http://molviz.org/pacupp">http://molviz.org/pacupp</a></p>
<p>Examples shown include:</p>
<ul>
<li>Coronoavirus SARS-CoV-2 spike protein cavity that is a
potential drug target
</li>
<li>Ribosome nascent peptide exit channel
</li>
<li>Proteasome
</li>
<li>HIV protease (detailed demonstration of PACUPP commands)
</li>
<li>Acetylcholinesterase catalytic pocket with inhibitor
</li>
<li>DNA, major and minor grooves</li>
<li>Orthogonal tunnels accessing the heme in protoglobin
</li>
<li>Oligopeptide-binding protein A with an octapeptide in a buried
cavity (detailed demonstration of PACUPP commands)</li>
</ul>
<p>-Eric</p>
<p>
</p>
<div style="-en-clipboard:true;">Eric Martz, Professor Emeritus,
Dept Microbiology (he/him/his)
</div>
<div>U Mass, Amherst -- <a href="http://martz.molviz.org/">Martz.MolviZ.Org</a>
</div>
<div>Guided Exploration of Macromolecules: <a
href="http://firstglance.jmol.org/">FirstGlance.Jmol.Org</a>
</div>
<div>Protein 3D Structure Wiki: <a href="http://proteopedia.org/">Proteopedia.Org</a>
</div>
<div>Top Five 3D MolVis Tools: <a href="http://top5.molviz.org/">Top5.MolviZ.Org</a>
</div>
<div>Education: Biochem in 3D at <a href="http://molviz.org/">MolviZ.Org</a>
</div>
<div>Find Functional Patches in Proteins: ConSurf.tau.ac.il
</div>
<div>Atlas of Macromolecules: <a href="http://atlas.molviz.org/">Atlas.MolviZ.Org</a>
</div>
<div>Interactive Molecules in Architectural Spaces: <a
href="http://molecularplayground.org/">MolecularPlayground.Org</a>
</div>
<div>Workshops: <a href="http://workshops.molviz.org/">Workshops.MolviZ.Org</a>
</div>
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